Contacts of the strand formed by residues 684 - 688 (chain A) in PDB entry 2V3V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A PRO* 3.6 39.0 - - + +
206A ARG* 4.0 19.1 - - + -
222A PRO* 3.8 13.9 - - + -
612A TYR* 3.5 24.9 - - + +
614A THR* 3.9 19.5 - - + -
646A ASN* 4.1 8.0 + - - +
649A ASP* 4.1 2.0 + - - +
680A CYS* 3.3 23.2 - - + +
681A ARG* 3.3 20.1 + - + +
682A PRO 3.3 0.2 - - - -
683A GLY* 1.3 80.6 - - - +
685A ILE* 1.3 85.1 + - - +
812A MGD 5.8 0.7 - - - +
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Residues in contact with ILE 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 3.9 22.9 - - + -
612A TYR 2.8 19.8 + - - +
613A LEU* 3.5 15.3 - - + -
614A THR* 2.9 27.8 + - - +
643A VAL* 3.9 7.2 - - + -
644A GLU 3.3 13.9 - - - +
645A ILE* 3.9 23.3 - - + -
649A ASP* 5.9 0.7 - - - +
663A VAL* 3.8 24.0 - - + -
680A CYS* 4.1 2.0 - - - -
684A LEU* 1.3 80.0 - - - +
686A ALA* 1.3 63.6 + - - +
718A ALA* 3.9 11.2 - - + -
720A VAL* 3.6 25.1 - - + -
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Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 4.0 7.2 - - - +
613A LEU* 4.6 0.2 - - - -
614A THR* 3.4 23.1 - - + -
616A MET* 3.9 9.8 - - + +
642A PHE 4.0 0.5 - - - +
643A VAL* 3.5 3.7 - - - +
644A GLU* 2.8 59.8 + - + +
680A CYS* 3.6 8.1 - - - -
685A ILE* 1.3 79.2 - - - +
687A VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 4.0 12.3 - - + -
614A THR 3.0 16.4 + - - +
615A SER* 3.1 26.0 - - - -
616A MET* 3.2 7.1 + - - +
642A PHE 3.7 3.8 - - - +
643A VAL* 3.9 12.3 - - + -
663A VAL* 5.1 3.8 - - + -
672A LEU* 3.6 28.0 - - + -
686A ALA* 1.3 80.1 - - - +
688A PRO* 1.4 68.3 - - + +
696A VAL* 3.7 32.1 - - + -
699A LEU* 5.1 2.7 - - + -
700A PHE* 3.9 15.5 - - + -
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Residues in contact with PRO 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A MET* 3.6 24.9 - - - +
618A VAL* 4.3 5.6 - - + -
641A ALA* 4.2 10.0 - - + +
642A PHE* 3.1 56.3 - - + +
687A VAL* 1.4 86.0 - - + +
689A PHE* 1.3 61.0 + - - +
690A PHE* 3.6 26.9 - - + -
691A ASP 5.4 0.2 + - - -
694A LYS 5.3 0.2 - - - +
696A VAL* 3.3 20.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il